1-11073981-G-C
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001998.3(EXOSC10):āc.2110C>Gā(p.Pro704Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000124 in 1,613,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 30)
Exomes š: 6.8e-7 ( 0 hom. )
Consequence
EXOSC10
NM_001001998.3 missense
NM_001001998.3 missense
Scores
1
18
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.96
Genes affected
EXOSC10 (HGNC:9138): (exosome component 10) Enables 3'-5'-exoribonuclease activity. Involved in several processes, including RNA catabolic process; maturation of 5.8S rRNA; and negative regulation of telomere maintenance via telomerase. Located in cytosol; nuclear lumen; and transcriptionally active chromatin. Part of nuclear exosome (RNase complex). [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.051965743).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXOSC10 | NM_001001998.3 | c.2110C>G | p.Pro704Ala | missense_variant | 19/25 | ENST00000376936.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXOSC10 | ENST00000376936.9 | c.2110C>G | p.Pro704Ala | missense_variant | 19/25 | 1 | NM_001001998.3 | P1 | |
EXOSC10 | ENST00000304457.11 | c.2082+250C>G | intron_variant | 1 | |||||
EXOSC10 | ENST00000474216.5 | n.1347C>G | non_coding_transcript_exon_variant | 7/13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151992Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251470Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135918
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461858Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 727236
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152110Hom.: 0 Cov.: 30 AF XY: 0.0000134 AC XY: 1AN XY: 74352
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
D;D;N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at